XR_001739605.2:n.664G>A

Variant names:

• chr2-98750023-G-A
• rs6751196
• XR_001739605.2:n.664G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001739605.2(LOC107985922):​n.664G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,064 control chromosomes in the GnomAD database, including 2,023 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2023 hom., cov: 32)
• Consequence: LOC107985922 XR_001739605.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 4 publications found

Genes affected

LOC107985922 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985922	XR_001739605.2	n.664G>A		non_coding_transcript_exon_variant	Exon 1 of 2
LOC107985922	XR_007087150.1	n.416-1297G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304199	ENST00000800925.1	n.188+614G>A		intron_variant	Intron 1 of 1
ENSG00000304199	ENST00000800926.1	n.56-32G>A		intron_variant	Intron 1 of 2
ENSG00000304199	ENST00000800927.1	n.-31G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23364 AN: 151946 Hom.: 2021 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0222

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.145

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.154 AC: 23363 AN: 152064 Hom.: 2023 Cov.: 32 AF XY: 0.150 AC XY: 11142 AN XY: 74358

African (AFR) AF: 0.196 AC: 8110 AN: 41434

American (AMR) AF: 0.122 AC: 1862 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3470

East Asian (EAS) AF: 0.0223 AC: 115 AN: 5162

South Asian (SAS) AF: 0.187 AC: 898 AN: 4812

European-Finnish (FIN) AF: 0.0802 AC: 850 AN: 10596

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10457 AN: 67986

Other (OTH) AF: 0.143 AC: 302 AN: 2110

Alfa AF: 0.154 Hom.: 3411

Bravo AF: 0.157

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.9
DANN	Benign	0.81
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6751196; hg19: chr2-99366486;